2021-03-01 

Trajectory Data for 
"A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms"
by
Marianne Grognot & Katja M. Taute*
Rowland Institute at Harvard
100 Edwin H Land Blvd
Cambridge, MA 02142
USA
*taute@rowland.harvard.edu

The article is currently under revision.
An earlier version of the manuscript is available at 
https://doi.org/10.21203/rs.3.rs-61942/v1


The two .mat files provide all trajectory data presented in the article in Matlab structure format. 
The file "EcoliTrajectories.mat" contains all E. coli trajectories.
The file "CcrescentusTrajectories.mat" contains all C. crescentus trajectories.
Trajectory position data are ADMM filtered as described in the Methods section of the manuscript.

Each file contains multiple Matlab structures starting with "V_", each corresponding to one dataset. 

Each structure V contains the following fields:
* V.Speeds is a cell array where each cell corresponds to one trajectory. The trajectory is described by an array with the following columns:
	- column 1: frame number
	- column 2-4 : x, y and z positions (in micrometers)
	- column 6-8 : instantaneous speed in x, y and z (micrometer per second)
	- column 9 : absolute value of instantaneous speed (micrometer per second)
	- column 10 : angular change in direction between frames (degrees)
* V.Parameters is a simplified structure with descriptive parameters, containing only the field V. parameters.fps which gives the frame rate of the acquisitions (frames per second)




***** EcoliTrajectories.mat *****

Three types of V structures are given (with reference to the datasets detailed in SI Table 2):

1) All motile trajectories in dataset "Speed in reservoirs over time", named in format "V_XXmin" where XX stands for the delay time.  

2) all motile trajectories from biological replicates in 10 µM/mm MeAsp gradients
format V_MeAspX_MMDD with 
		. X being the # of the biological replicate at that date (if several replicates within the day)
		. MMDD date of experiment
		. "_bulk" or nothing at the end. Those ending in "_bulk" contain only trajectory segments with a distance of at least 10 µm from the surface.

3) Control experiments with different MeAsp gradients (dataset "Geometry tests MeAsp')
	* V_MeAsp_1mM_0512_bulk 1 mM/mm
	* V_MeAspInverted_1mM_0512_bulk -1 mM/mm
	* V_Reference_0503_bulk 0 mM/mm



***** CcrescentusTrajectories *****

Two types of V structures are given :
1) all motile bulk trajectories sorted by biological replicate, named after the date of experiment V_MMDD

2) trajectories sorted by analysis subsets (v)
		. V all trajectories combined (set #1)
		. V_motilebulk (set #2)
		. V_analyzed trajectories on which we run turn detection (set #3)
		. V_smooth smooth swimmers (set #4)
		. V_1turnormore 1+ turn detected (set #5)
		. V_1runormore 1+ run detected (set #6)
		. V_1idrunormore 1+ run identified as a forward or backward (set #7)
		. V_1FWand1BWormore trajectories with at least of backward and one forward (set #8)
